Research

Research Areas

Despite the availability of the human genome sequence and the ever-accelerating pace of biomedical research, the root causes of common human diseases remain largely unknown. The ability to sequence the genomes of a large number of affected individuals and controls would allow us to examine all the genetic differences to search for the molecular etiology of a variety of diseases. Identifying the causal genes and variants would represent a significant step towards improved diagnosis, prevention and treatment of disease. Recently, NIH has initiated an international effort to develop a revolutionary technology that will enable the rapid sequencing of a human genome for as little as $1000. As part of this international effort, we are developing a new paradigm to achieve unprecedented multiplexing, parallelization and miniaturization so that hundreds of millions of DNA samples can be manipulated in a single integrated device.

We are investigating several fundamentally different strategies for DNA sequencing. The image on the left illustrates the basic concepts of sequencing by denaturation (SBD), a novel sequencing technology that involves real-time monitoring of the melting profiles of dideoxy-terminated oligonucleotides on surface-bound clones. The stepwise decay in fluorescent intensity is used to decode the sequence information.

We are developing various technologies for rapid, inexpensive, and high-throughput biomolecular analyses. The image on the left is an illustration of a high-density microbead array capable of supporting these types of studies. The beads can be conjugated to various biomolecules and then assembled in an ordered fashion onto a microfabricated chip at densities in the tens of millions of beads per square centimeter.

We are designing and assembling automated imaging systems using state-of-the-art technology. The image on the left is an illustration of a biomolecular analysis platform mounted on a high-speed piezo-electric stage with nanometer-scale positioning accuracy. The microscope objective is also mounted to a piezo-electric drive to enable rapid auto-focusing capabilities. Other critical components not shown in this figure include extremely sensitive cameras containing electron-multiplying charge-coupled devices (EMCCD), lasers, and ultra-high-speed wavelength switchers.

We are exploring numerous approaches to derivatize, modify, conjugate, enhance, and/or passivate surfaces, biomolecules, microbeads, and nanoparticles. In the figure on the left, a glass coverslip derivatized with biotin moieties is used to capture a streptavidin-coated microbead conjugated to DNA molecules. This type of platform can support a wide variety of applications such as DNA sequencing, genotyping, and DNA-protein interaction studies. The surface chemistry plays a crucial role in our detection schemes by minimizing non-specific binding and thus increasing sensitivity.

We are developing new approaches fragmenting, modifying, and amplifying genomic DNA. These sample preparation steps are critical in a majority of genomic analysis schemes, including genome sequencing. The figure on the left is an illustration of a process known as hyperbranched rolling circle amplification (HRCA). This type of DNA amplification scheme is an isothermal alternative to the polymerase chain reaction (PCR). Circularized DNA molecules are used to create a set of tandem repeats of different lengths.

We are designing and fabricating various microfluidic flow cells and devices to support our high-throughput genomic and proteomic platforms. The figure on the left is an exploded view of a protein or DNA microarray enclosed within a microfluidic chamber. The flow cell enables us to perform a series of biochemical reactions on the chip in an automated fashion.

We are exploring a number of different strategies that will enable us to detect single molecule events. Attaching the molecules of interest to specialized nanoparticles allow us to image molecular interactions using conventional microscopy. The image on the left is an example of such a nanoparticle conjugated to a single oligonucleotide.

We are engineering proteins with new and improved functions and activities using rational design and directed evolution. These modified proteins can be used to catalyze specialized reactions that are inefficient or impossible using native proteins.

We are interested in modeling the various physical and biochemical phenomena that we often observe in the laboratory setting. These include biochemical reactions, microfluidics, electric and magnetic fields, heat transfer, diffusion, and molecular interactions.